Police spokesman Goran Gunnarsson told the Swedish news agency TT that police received a call from someone who heard the boys screaming.
The unidentified woman apprehended at the scene is believed to be a relative of the two boys.
Charges against her include suspicion of aggravated assault since it is illegal to perform a circumcision in Sweden without supervision by a medical professional.
The Swedish Parliament passed a law in 2001 requiring a professional to be present at all circumcisions.
The law is not only designed to safeguard against pain but also to help prevent potential infection.